Sequencing DNA in Space

NASA is not often known for making the best use of existing COTS (commercial off the shelf technology) aboard the ISS. Then again, sometimes they are. This is an example of when the agency really grabs cutting edge biotech and sends it into space.

There's usually quite a lag time. The reasons range from slogging through the often cumbersome payload safety and integration process to people at NASA who are simply not up to date with what the ral world is doing in their field. In this instance a rather remarkable gizmo is being flown in space that truly puts genetic sequencing in the palm of your hand. Indeed, its almost as if NASA was flying part of a version 1.0 Tricorder in space. This is cutting edge technology folks.

Keith's update: I got very informative responses to my inquiry from Aaron Burton at the NASA JSC Astromaterials Research and Exploration Science Division and from Sarah Castro, NASA JSC Biomedical Research and Environmental Sciences Division. Scroll to the end of the article for these responses. Below is an annotated and enhanced illustration version of an article NASA originally posted several months ago.

A tiny new device called the MinION, developed by Oxford Nanopore Technologies, promises to help scientists sequence DNA in space. NASA's Biomolecule Sequencer investigation is a technology demonstration of the device.

The investigation's objectives include providing proof-of-concept for the device's functionality and evaluation of crew operability of a DNA sequencer in the International Space Station's microgravity environment. While the petite device is already being used to sequence DNA on Earth, it has never been used to do so in space.

NASA minION flight hardware for the ISS experiments. Note that this payload is so small that the standard NASA property tag is almost the same size as the payload itself. Credit: NASA/Sarah Castro

Determining the sequence of DNA is a powerful way to characterize organisms and determine how they are responding to changes in the environment. The goal of this technology demonstration is to provide evidence that DNA sequencing in space is possible, which holds the potential to enable the identification of microorganisms, monitor changes in microbes and humans in response to spaceflight, and possibly aid in the detection of DNA-based life elsewhere in the universe.

"The ultimate goal is to be able to do on the space station or on Mars the things we are able to do normally on Earth when we sequence DNA," said investigator Douglas Botkin, Ph.D. "We want to replicate the laboratory environment, the high-tech equipment and those processes we use terrestrially, and try to demonstrate that functionality in a microgravity environment."

This has never been done in space before and, if successful, this little device could be a big deal.

"Currently aboard the space station there is not a real-time method for identifying microbes, diagnosing infectious disease, and collecting any form of genomic and genetic data concerning crew health," said NASA Microbiologist and Project Manager Sarah Castro, Ph.D. "Meeting these needs relies on returning samples from space to Earth and subsequent ground-based analysis, which takes time. Real-time analysis could inform scientific investigations, measure the impact of spaceflight on the human body, inform medical interventions and define the effectiveness of countermeasures.

"You can look at DNA for permanent changes, what spaceflight is doing to your DNA long-term, but also by looking at the RNA, you can see how the human body or other organisms are reacting in real time," said Principal Investigator Aaron Burton, Ph.D.

The MinION DNA sequencer sits atop a state-of-the-art next-generation sequencer. The MinION is significantly smaller than typical laboratory sequencers that are less conducive to spaceflight. Credits: Sarah Castro

During the investigation, crew members will sequence the DNA of bacteria, bacteriophage (a virus that infects and replicates within a bacterium) and rodents from samples prepared on Earth that have known genomic characteristics. Researchers on Earth also will run synchronous ground controls to evaluate how well the hardware is working.

"We absolutely believe that the sequencer will perform successfully in the microgravity environment of space," said Deputy Project Manager and Project Engineer Kristen John, Ph.D.

In nanopore sensing, just as water flows through a drain, an ionic current flows through a nanopore. When molecules pass through the hole the current is disrupted in characteristic ways, similar to the way the water flow would change if you placed objects in the drain Credits: nanoporetech.com

The tiny, plug and play sequencer about the size of a large candy bar is diminutive compared to the large microwave-sized sequencers used on Earth.

"Most sequencers in Earth-based labs involve optics, fluorescence, lasers and other vibration sensitive components that are not suited for spaceflight or microgravity," said Castro. "There is huge power consumption at play with those as well."

Conversely, the compact biomolecule sequencer has minimal moving parts and plugs directly into a laptop or tablet, which supplies power to the device and collects the sequencing data.

The data is collected as the device passes an ionic current through a perforated surface containing nanopores (natural cell membrane ion pores) and measures the changes in the current as biological molecules from samples pass through the pores. The change in current can be used to identify a DNA sequence or other molecules.

Unlike terrestrial instruments whose sequencing run times can take days, this device's data is available in near real time; analysis can begin within 10-15 minutes from the application of the sample.

If successful, this investigation will allow the implementation of the sequencer into operational microbial monitoring, a vast array of medical operations, a research facility on the ISS and integration into astrobiology-based exploration missions.

"The space station and Earth are end members of the gravity continuum, so if the device works on Earth and in microgravity, then it should work in any environment in between like an asteroid or Mars," said Burton.

This DNA sequencer is also being tested for diagnostics on Earth. The development of robust procedures for the operation of this device in low-resource environments has direct relevance to field deployment on Earth, such as for medical operations in the regions where immediate access to a full laboratory is not available. Data collected from this investigation may be useful toward additional development of the device. Additionally, maintaining the sequencer as a research facility on the space station holds the potential to support an immeasurable number of scientific investigations, any of which could have Earth-based applications.

Keith's note: This article is an original NASA.gov posting enhanced with additional illustrations and reference links. I have sent NASA the following request for additional information. "This is very cool stuff and using the MinION DNA sequencer is a paradigm shifting move on NASA's part. This technology has applicability not only to crew health/safety and life support but also advanced technology development and astrobiology (life detection/characterization). Can you provide me with pictures of the actual flight hardware that NASA will be flying to ISS? Can you also tell me when this device will be activated and specifically what organisms you intend to sequence? When will results from this investigation be published - and where will they be published? Will interim results prior to the completion of the investigation be released - and if so when/where will they be released? Is CASIS involved in this activity? Is the NASA Astrobiology Institute involved?"

Meanwhile CASIS has a competing system "Genes in Space" to do genomics on orbit using minipcr proprietary technology. As best I can tell (and I have asked for more information) the NASA JSC minIOn and CASIS minipcr based efforts are separate. They make no mention of each other. The NASA Genelab web portal makes no mention of either genomic project. Yet Genelab does have interaction with Twins in Space effort which includes genomics studies. When I asked the Genelab folks at the recent American Society for Gravitational and Space Research meeting why NASA's various genomics projects are not coordinated no one had an answer. And NASA's Astrobiology Institute (which has a great interest in genomics) has zero interactions that have been made public. More stove piping at NASA.

Keith's update: I got the following response to my inquiry from Aaron Burton at the NASA JSC Astromaterials Research and Exploration Science Division:

"The [minION] sequencer is currently manifested on SpaceX 9, which has a launch date of June 24th, 2016, though the launch dates have been moving quite a bit. The flow cells are best if used within 60 days of their production, so we're looking at doing the sequencing in the June to August timeframe, and the data should hopefully be back on Earth a few days after each sample run.

We are sending up samples that we are preparing on the ground, and the crew will thaw the samples and load them for sequencing. The samples will contain lambda bacteriophage, which is Oxford Nanopore Technology's characterization standard for sequencer performance. The samples will also contain E. coli and mouse genomic DNA to demonstrate that you could sequence DNA from any organism. The samples will not contain human DNA.

We plan to submit papers arising from this work to Nature Microgravity, with open access. Hopefully we'll be able to get the paper submitted within a month or two after we get the data back. Depending on journal policies (I haven't contacted them about this yet), we would like to post the data (either the base-called sequences or the raw data) on the NASA GeneLab site to make it available to any interested parties. We will work with the journal to see about when we might be able to post the data on GeneLab, assuming they're okay with it.

CASIS is not involved with this activity, though we're definitely aware of the mini-PCR effort. PCR is certainly a complimentary technology to sequencing, and, particularly for environmental monitoring, we'll likely need to do some amplification to detect organisms, as the ISS is a pretty clean environment.

The project is being supported by JSC center level funding only, and is not receiving funds from the NASA Astrobiology Institute. However, I am a collaborator on the NASA Goddard NAI node, and was a postdoc at NASA Goddard when we started thinking about using sequencing in space exploration. We are working on astrobiology-focused applications for Nanopore sequencing, though that work is at a very preliminary stage."

Keith's update: I received additional feedback from Sarah Castro, NASA JSC Biomedical Research and Environmental Sciences Division: "No, we did not modify the sequencers at all. They are 100% COTS. JSC is rolling out a new Class 1-E flight hardware certification process that utilizes efficiencies learned over the years to reduce the time it takes to get payloads to the ISS. We were actually selected and funded to demonstrate this new 1-E process. We received authority to proceed last February and turned over our flight hardware in December. While the Class 1-E process lessens much of the paperwork, the safety requirements needed for flight certification were not changed. As payload developers, we appreciate the level of scrutiny given toward safety, as well as the leveraging of past lessons learned to remove redundancies in other areas of the certification process. Aaron, Kristen, and I are all scientists at JSC, so we valued the flexibility of the 1-E process in that we were able to focus on the science while working toward hardware delivery without being totally consumed by the process.

We are still employing culture-based techniques for our microbial monitoring efforts, and bringing about a way to identify and diagnose microbial issues in-flight is one of my utmost goals. As Aaron mentioned, we are sending up ground-prepared samples to demonstrate sequencing in microgravity. We have high hopes for the sequencer, and with the ultimate goals including environmental monitoring, human health-related research, and astrobiology, we knew the importance of working toward the ability to go from a swab to a sequence. Therefore, we have been working on a spaceflight-compatible sample preparation process that will be analog tested this summer during the NEEMO 21 mission. We are using the miniPCR to perform our amplifications, as it fits within our spaceflight-compatible scheme and will be on the ISS."

"A nanopore is a nano-scale hole. In its devices, Oxford Nanopore passes an ionic current through nanopores and measures the changes in current as biological molecules pass through the nanopore or near it. The information about the change in current can be used to identify that molecule."

"The objectives of Biomolecule Sequencer are to (1) provide proof-of-concept for the functionality and (2) evaluate crew operability of a DNA sequencer in the space environment. The immediate capabilities from the sequencer are, but are not limited to, in-flight microbial identification for crew and vehicle health assessments; monitoring changes at the DNA level in astronauts and microbes; and analyzing DNA-based life on other worlds if present. Molecular biology is a branch of biology aimed at understanding the molecular basis of biological activity at the level of DNA, RNA, and proteins. One of the most powerful applications of molecular biology techniques is in the identification of organisms; identification can be achieved using a variety of methods, each with their own advantages and disadvantages.

ISS Expedition Duration: March 2016 - September 2016"

"The miniaturized DNA sequencer is a COTS device developed by Oxford Nanopore Technologies and implements a method of DNA sequencing unlike any instrument currently on the market. The device measures changes in electrical current through a nanopore that is dependent on the sequence of the DNA strand that is passing through it. Because the technology is built on ion pores that are on the nanometer scale, the hardware itself is exceptionally small (9.5 x 3.2 x 1.6 centimeters), lightweight (less than 120 grams with USB cable), and powered only though connection to a laptop or tablet. The sequencing device is permanent, while the flow cells, to which the samples are added, are periodically replaced."

"Geneticists Andrew Feinberg and Lindsay Rizzardi have successfully administered genome sequencing in zero-gravity. They wanted to test out if zero-gravity is a viable environment for long-term storage of genetic material, and whether pipettes are needed to transfer a layer of centrifuged blood to another vessel. They used positive displacement pipettes, which are essentially small plungers that directly touch the sample. The tip of the pipette was also small enough to not let any air in and to not let any fluid spill which are important feats while in zero-gravity. Feinberg and Rizzardi tried to other methods, but this one proved to be the most effective."

"As a first step toward evaluating the performance of nanopore sequencers in a microgravity environment, we tested the Oxford Nanopore Technologies MinIONTM in a parabolic flight simulator to examine the effect of reduced gravity on DNA sequencing. The instrument successfully generated three reads, averaging 2,371 bases. However, the median current was shifted across all reads and the error profiles changed compared with operation of the sequencer on the ground, indicating that distinct computational methods may be needed for such data."

"Here, we describe a first look at our in-flight concept of operations (sample loading, tablet set-up, etc.) and the performance of the MinIONTM sequencer under the intermittent microgravity conditions that occur on a microgravity parabolic flight. Although the present experiments were performed with sequencing libraries that were prepared on the ground, we posit that library preparation could also be performed in space with the liquid handling procedures described in Rizzardi et al. (2015)."

"Figure 1: a) The MinIONTM flow cell, which was loaded into the device prior to the parabolic flight. The white arrow marks vents, which leaked during return transport to the Johnson Space Center. b) Loading the library onto the MinIONTM. Angling the pipette perpendicular to the pore was necessary to avoid introducing air bubbles. c) The MinIONTM setup on the plane. The flow cell was connected to a tablet running Oxford Nanopore Technologies' MinKNOWTM sequencing software via a USB 3.0 cable. We noted significant glare off of the tablet screen."

NASA is not often known for making the best use of existing COTS (commercial off the shelf technology) aboard the ISS. Then again, sometimes they are. This is an example of when the agency really grabs cutting edge biotech and sends it into space.